Interface & Visualization

.gitignore

@@ -102,3 +102,9 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+# node modules
+node_modules/
+
+# test snapshots
+_snapshots_

app/Meta.py

@@ -136,14 +136,15 @@ def insert_sites(fileName,shp_file,dbf_file,prj_file,shx_file):
         for index, row in data_g.iterrows():
             flat_list = []
             for pt in list(row['geometry'].exterior.coords):
-                pt=pt+(115,)
+                if len(pt) < 3:
+                    pt=pt+(115,)
                 flat_list.append(pt)
             poly = Polygon(flat_list)
             data.loc[index, 'geometry'] = poly
 
         if(all(x in accepted_columns for x in columns)):
             data['time_zone'].fillna("America/Phoenix", inplace = True)
-            data['soilnotes'].fillna("some text", inplace = True)      
+            data['soilnotes'].fillna("", inplace = True)      
             data['greenhouse'].fillna("f", inplace = True)            
             data=data.fillna('')
             file_name='sites_n.csv'
@@ -182,6 +183,8 @@ def insert_sites(fileName,shp_file,dbf_file,prj_file,shx_file):
         os.remove(dbf_file_target)
         os.remove(prj_file_target)
         os.remove(shx_file_target)                
+        os.remove(file_name)        
+
 
 def insert_treatments(username,fileName):
     """
@@ -555,4 +558,4 @@ def insert_citationsSites(fileName):
     except Exception :
         # Logs the error appropriately
         logging.error(traceback.format_exc())
-        return 410
+        return 410

client/Dockerfile

@@ -4,6 +4,8 @@ COPY . /code
 
 WORKDIR /code
 
-RUN pip install -r requirements.txt    
+RUN pip install -r requirements.txt &&  pip install -U flask-cors
+
+EXPOSE 6000
 
 CMD ["python","client.py"]

client/client.py

@@ -6,16 +6,20 @@
 from flask import Flask, g, render_template,request,redirect,Response,flash,jsonify, make_response
 from flask import request
 
+import logging
 import json
 from time import sleep
+import sys
+from flask_cors import CORS, cross_origin
 
 # Create app
 app = Flask(__name__)
 app.secret_key = 'my unobvious secret key'
 
 # The maximum allowed payload to 16 megabytes.
 app.config['MAX_CONTENT_LENGTH'] = 16 * 1024 * 1024
-
+cors = CORS(app, resources={r'/*': {'origins': '*'}})
+logging.getLogger('flask_cors').level = logging.DEBUG
 
 ALLOWED_EXTENSIONS = set(['csv', 'xls','xlsx'])
 

input_files/citations_sites.csv

@@ -1,2 +1,2 @@
 author,year,title,sitename
-LeBauer,2010,Expert Prior,MAC Field Scanner Season 4 Range 51 Column 7 E
+LeBauer,2010,Expert Prior,MAC Field Scanner Season 8 Range 1 Column 1 W

input_files/experiments_sites.csv

@@ -1,6 +1,6 @@
 experiment_name,sitename
-MAC Season 8: Border ,MAC Field Scanner Season 5 Range 39 Column 1 E
-MAC Season 8: Uniformity ,MAC Field Scanner Season 5 Range 39 Column 2 E
-MAC Season 8: DP4 ,MAC Field Scanner Season 5 Range 39 Column 3 E
-MAC Season 8: DP ,MAC Field Scanner Season 5 Range 39 Column 4 E
-MAC Season 8: DP test,MAC Field Scanner Season 5 Range 39 Column 5 E
+MAC Season 8: Border ,MAC Field Scanner Season 8 Range 20 Column 1 W
+MAC Season 8: Uniformity ,MAC Field Scanner Season 8 Range 20 Column 1 E
+MAC Season 8: DP4 ,MAC Field Scanner Season 8 Range 20 Column 2 W
+MAC Season 8: DP ,MAC Field Scanner Season 8 Range 20 Column 2 E
+MAC Season 8: DP test,MAC Field Scanner Season 8 Range 20 Column 3 W

input_files/experiments_treatments.csv

@@ -1,6 +1,6 @@
 experiment_name,treatment_name
-MAC Season 8: Border ,MAC Season 6: Sorghum
-MAC Season 8: Uniformity ,MAC Season 7: Sorghum Aug
-MAC Season 8: DP4 ,MAC Sorghum Season 4
-MAC Season 8: DP ,MAC Sorghum Season 2
-MAC Season 8: DP test,MAC Season 5: Winter Wheat
+MAC Season 8: Border ,No irrigation
+MAC Season 8: Uniformity ,Well watered
+MAC Season 8: DP4 ,Well watered
+MAC Season 8: DP ,No irrigation
+MAC Season 8: DP test,Well watered

input_files/sites_cultivars.csv

@@ -1,2 +1,2 @@
 cultivar_name,specie_id,sitename
-Orita,2588,MAC Field Scanner Season 8 Range 1 Column 1 W
+DP_074,2588,MAC Field Scanner Season 8 Range 1 Column 1 W

input_files/treatments.csv

@@ -1,3 +1,3 @@
 name,definition,control
 No irrigation,some text,f
-Well watered,some text,f
+Well watered,some text,f

interface/README.md

@@ -0,0 +1,76 @@
+This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
+
+## Available Scripts
+
+### Install the Project dependencies
+
+ Before running the project, run:
+
+### `yarn`
+
+This will install all the dependencies of the project.
+
+### In the project directory, you can run:
+
+### `yarn start`
+
+Runs the app in the development mode.<br />
+Open [http://localhost:3000](http://localhost:3000) to view it in the browser.
+
+The page will reload if you make edits.<br />
+You will also see any lint errors in the console.
+
+### `yarn test`
+
+Launches the test runner in the interactive watch mode.<br />
+See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
+
+### `yarn build`
+
+Builds the app for production to the `build` folder.<br />
+It correctly bundles React in production mode and optimizes the build for the best performance.
+
+The build is minified and the filenames include the hashes.<br />
+Your app is ready to be deployed!
+
+See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
+
+### `yarn eject`
+
+**Note: this is a one-way operation. Once you `eject`, you can’t go back!**
+
+If you aren’t satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
+
+Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you’re on your own.
+
+You don’t have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn’t feel obligated to use this feature. However we understand that this tool wouldn’t be useful if you couldn’t customize it when you are ready for it.
+
+## Learn More
+
+You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
+
+To learn React, check out the [React documentation](https://reactjs.org/).
+
+### Code Splitting
+
+This section has moved here: https://facebook.github.io/create-react-app/docs/code-splitting
+
+### Analyzing the Bundle Size
+
+This section has moved here: https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size
+
+### Making a Progressive Web App
+
+This section has moved here: https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app
+
+### Advanced Configuration
+
+This section has moved here: https://facebook.github.io/create-react-app/docs/advanced-configuration
+
+### Deployment
+
+This section has moved here: https://facebook.github.io/create-react-app/docs/deployment
+
+### `yarn build` fails to minify
+
+This section has moved here: https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify

interface/package.json

@@ -0,0 +1,59 @@
+{
+  "name": "metadata_upload_interface",
+  "version": "0.1.0",
+  "private": true,
+  "dependencies": {
+    "@testing-library/jest-dom": "^4.2.4",
+    "@testing-library/react": "^9.3.2",
+    "@testing-library/user-event": "^7.1.2",
+    "@turf/turf": "^5.1.6",
+    "d3": "^5.16.0",
+    "enzyme": "^3.11.0",
+    "enzyme-adapter-react-16": "^1.15.2",
+    "enzyme-to-json": "^3.5.0",
+    "google-spreadsheet": "^3.0.11",
+    "google-spreadsheet-to-json": "^1.0.0",
+    "google-spreadsheets-key-parser": "^1.1.0",
+    "googleapis": "^39.2.0",
+    "jquery": "^3.5.1",
+    "jsdom": "^16.2.2",
+    "leaflet": "^1.6.0",
+    "papaparse": "^5.2.0",
+    "pretty": "^2.0.0",
+    "react": "^16.13.1",
+    "react-dom": "^16.13.1",
+    "react-dropzone": "^11.0.1",
+    "react-leaflet": "^2.7.0",
+    "react-router-dom": "^5.1.2",
+    "react-scripts": "3.4.1",
+    "shpjs": "^3.5.0",
+    "swr": "^0.2.3",
+    "tabletop": "^1.6.3"
+  },
+  "jest": {
+    "snapshotSerializers": [
+      "enzyme-to-json/serializer"
+    ]
+  },
+  "scripts": {
+    "start": "react-scripts start",
+    "build": "react-scripts build",
+    "test": "react-scripts test",
+    "eject": "react-scripts eject"
+  },
+  "eslintConfig": {
+    "extends": "react-app"
+  },
+  "browserslist": {
+    "production": [
+      ">0.2%",
+      "not dead",
+      "not op_mini all"
+    ],
+    "development": [
+      "last 1 chrome version",
+      "last 1 firefox version",
+      "last 1 safari version"
+    ]
+  }
+}

interface/public/index.html

@@ -0,0 +1,45 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="theme-color" content="#000000" />
+    <meta
+      name="description"
+      content="Web site created using create-react-app"
+    />
+    <link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
+    <!--
+      manifest.json provides metadata used when your web app is installed on a
+      user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
+    -->
+    <link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
+    <!--
+      Notice the use of %PUBLIC_URL% in the tags above.
+      It will be replaced with the URL of the `public` folder during the build.
+      Only files inside the `public` folder can be referenced from the HTML.
+
+      Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
+      work correctly both with client-side routing and a non-root public URL.
+      Learn how to configure a non-root public URL by running `npm run build`.
+    -->
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" />
+    <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/leaflet.css" integrity="sha512-xwE/Az9zrjBIphAcBb3F6JVqxf46+CDLwfLMHloNu6KEQCAWi6HcDUbeOfBIptF7tcCzusKFjFw2yuvEpDL9wQ==" crossorigin="" />
+    <title>React App</title>
+  </head>
+  <body>
+    <noscript>You need to enable JavaScript to run this app.</noscript>
+    <div id="root"></div>
+    <!--
+      This HTML file is a template.
+      If you open it directly in the browser, you will see an empty page.
+
+      You can add webfonts, meta tags, or analytics to this file.
+      The build step will place the bundled scripts into the <body> tag.
+
+      To begin the development, run `npm start` or `yarn start`.
+      To create a production bundle, use `npm run build` or `yarn build`.
+    -->
+  </body>
+</html>

interface/src/App.css

@@ -0,0 +1,38 @@
+.App {
+  text-align: center;
+}
+
+.App-logo {
+  height: 40vmin;
+  pointer-events: none;
+}
+
+@media (prefers-reduced-motion: no-preference) {
+  .App-logo {
+    animation: App-logo-spin infinite 20s linear;
+  }
+}
+
+.App-header {
+  background-color: #282c34;
+  min-height: 100vh;
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  justify-content: center;
+  font-size: calc(10px + 2vmin);
+  color: white;
+}
+
+.App-link {
+  color: #61dafb;
+}
+
+@keyframes App-logo-spin {
+  from {
+    transform: rotate(0deg);
+  }
+  to {
+    transform: rotate(360deg);
+  }
+}